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Table 3 WINGS input/output datasets for each component-type within our clinical omics use-case

From: Use of semantic workflows to enhance transparency and reproducibility in clinical omics

Component-type Input dataset(s) Output dataset(s)
CreateLocalCOSMIC GeneTrails_Genes COSMICSubset
CreateLocalSNP GeneTrails_Genes SNPSubset
QueryLocalCOSMIC Patient_Called_DNA_Variant_File, COSMICSubset Queried_COSMIC_Result
QueryLocalSNP Patient_Called_DNA_Variant_File, SNPSubset Queried_SNP_Result
PredictProteinConsequence Patient_Called_DNA_Variant_File, Transcript_File Predicted_Protein_Consequence
MergeAnnotation Pateint_Called_Variant_File, Queried_COSMIC_Result, Queried_SNP_Result, Predicted_Protein_Consequence, In_House_Curation_of_DNA_Variants Final_Annotation_of_DNA_Variants